It is chronicled that Sabiniano Manrique de Lara (1653–63), who arrived in the galleon San Francisco Xavier with the Archbishop Poblete, refused to disembark until this dignitary had blessed the earth he was going to tread. It was he too who had the privilege of witnessing the expurgation of the Islands of the excommunications and admonitions of Rome. The Archbishop brought peace and goodwill to all men, being charged by His Holiness to sanctify the Colony.

The ceremony was performed with great solemnity, from an elevation, in the presence of an immense concourse of people. Later on, the pious Governor Lara was accused of perfidy to his royal master, and was fined ₱60,000, but on being pardoned, he retired to Spain, where he took holy orders.

His successor, Diego Salcedo (1663–68), was not so fortunate in his relations with Archbishop Poblete, for during five years he warmly contested his intervention in civil affairs. Poblete found it hard to yield the exercise of veto in all matters which, by courtesy, had been conceded to him by the late Governor Lara. The Archbishop refused to obey the Royal Decrees relating to Church appointments under the Royal patronage, such preferments being in the hands of the Gov.-General as vice-royal patron. These decrees were twice notified to the Archbishop, but as he still persisted in his disobedience, Salcedo signed an order for his expulsion to Marivéles. This brought the prelate to his senses, and he remained more submissive in future. It is recorded that the relations between the Governor and the Archbishop became so strained that the latter was compelled to pay a heavy fine—to remain standing whilst awaiting an audience—to submit to contumely during the interviews—and when he died, the Governor ordered royal feasts to celebrate the joyful event, whilst he prohibited the de profundis Mass, on the ground that such would be inconsistent with the secular festivities.

The King, on being apprised of this, permitted the Inquisition to take its course. Diego Salcedo was surprised in his Palace, and imprisoned by the bloodthirsty agents of the Santo Oficio. Some years afterwards, he was shipped on board a galleon as a prisoner to the Inquisitors of Mexico, but the ship had to put back under stress of weather, and Salcedo returned to his dungeon. There he suffered the worst privations, until he was again embarked for Mexico. On this voyage he died of grief and melancholy. The King espoused the cause of the ecclesiastics, and ordered Salcedoʼs goods, as well as those of his partisans, to be confiscated.

Manuel de Leon (1669–77) managed to preserve a good understanding with the clergy, and, on his decease, he bequeathed all his possessions to the Obras Pias (q.v.).

Troubles with the Archbishop and friars were revived on the Government being assumed by Juan de Nárgas (1678–84). In the last year of his rule, the Archbishop was banished from Manila. It is difficult to adequately appreciate the causes of this quarrel, and there is doubt as to which was right—the Governor or the Archbishop. On his restoration to his See, he was one of the few prelates—perhaps the only one—who personally sought to avenge himself. During the dispute, a number of friars had supported the Government, and these he caused to stand on a raised platform in front of a church, and publicly recant their former acts, declaring themselves miscreants. Juan de Nárgas had just retired from the Governorship after seven yearsʼ service, and the Archbishop called upon him likewise to abjure his past proceedings and perform the following penance:—To wear a penitentʼs garb—to place a rope around his neck, and carry a lighted candle to the doors of the cathedral and the churches of the Parian, San Gabriel and Binondo, on every feast day during four months. Nargas objected to this degradation, and claimed privilege, arguing that the Archbishop had no jurisdiction over him, as he was a Cavalier of the Military Order of St. James. But the Archbishop only desisted in his pretensions to humiliate Nárgas when the new Governor threatened to expel him again.

Fernando Bustamente Bustillo y Rueda (1717–19) adopted very stringent measures to counteract the Archbishopʼs excessive claims to immunity. Several individuals charged with heinous crimes had taken church asylum and defied the civil power and justice. The Archbishop was appealed to, to hand them over to the civil authorities, or allow them to be taken. He refused to do either, supporting the claim of immunity of sanctuary. At the same time it came to the knowledge of the Governor that a movement had been set on foot against him by those citizens who favoured the Archbishopʼs views, and that even the friars had so debased themselves as to seek the aid of the Chinese residents against the Governor. José Torralba (q.v.), the late acting-Governor, was released from confinement by the Governor, and reinstated by him as judge in the Supreme Court, although he was under an accusation of embezzlement to the extent of ₱700,000. The Archbishop energetically opposed this act. He notified to Torralba his excommunication and ecclesiastical pains, and, on his own authority, attempted to seize his person in violation of the privileges of the Supreme Court. Torralba, with his sword and shield in hand, expelled the Archbishopʼs messenger by force. Then, as judge in the Supreme Court, he hastened to avenge himself of his enemies by issuing warrants against them. They fled to Church asylum, and, with the moral support of the Archbishop, laughed at the magistrates. There the refugees provided themselves with arms, and prepared for rebellion. When the Archbishop was officially informed of these facts, he still maintained that nothing could violate their immunity. The Governor then caused the Archbishop to be arrested and confined in a fortress, with all the ecclesiastics who had taken an active part in the conspiracy against the Government.

Open riot ensued, and the priests marched to the Palace, amidst hideous clamourings, collecting the mob and citizens on the way. It was one of the most revolting scenes and remarkable events in Philippine history. Priests of the Sacred Orders of Saint Francis, Saint Dominic, and Saint Augustine joined the Recoletos in shouting “Viva la Iglesia,” “Viva nuestro Rey Don Felipe Quinto.”[8] The excited rabble rushed to the Palace, and the Guard having fled, they easily forced their way in. One priest who impudently dared to advance towards the Governor, was promptly ordered by him to stand back. The Governor, seeing himself encircled by an armed mob of laymen and servants of Christ clamouring for his downfall, pulled the trigger of his gun, but the flint failed to strike fire. Then the crowd took courage and attacked him, whilst he defended himself bravely with a bayonet, until he was overwhelmed by numbers. From the Palace he was dragged to the common jail, and stabbed and maltreated on the way. His son, hearing of this outrage, arrived on horseback, but was run through by one of the rebels, and fell to the ground. He got up and tried to cut his way through the infuriated rioters, but was soon surrounded and killed, and his body horribly mutilated.

The populace, urged by the clerical party, now fought for the liberty of the Archbishop. The prison doors were broken open, and the Archbishop was amongst the number of offenders liberated. The prelate came in triumph to the Palace, and assumed the Government in October, 1719. The mob, during their excesses, tore down the Royal Standard, and maltreated those whom they met of the unfortunate Governorʼs faithful friends. A mock inquiry into the circumstances of the riot was made in Manila in apparent judicial form. Another investigation was instituted in Mexico, which led to several of the minor actors in this sad drama being made the scapegoat victims of the more exalted criminals. The Archbishop held the Government for nine years, and was then transferred to the Mexican Bishopric of Mechoacan.

Pedro Manuel de Arandia (1754–59) is said to have expired of melancholy, consequent, in a measure, on his futile endeavours to govern at peace with the friars, who always secured the favour of the King.